org.utgenome.gwt.utgb.client.bio
Class InfoSilkGenerator

java.lang.Object
  extended by org.utgenome.gwt.utgb.client.bio.GenomeRangeVisitorBase
      extended by org.utgenome.gwt.utgb.client.bio.InfoSilkGenerator
All Implemented Interfaces:
GenomeRangeVisitor

public class InfoSilkGenerator
extends GenomeRangeVisitorBase

Generating read information in Silk format, which is used for displaying mouse over message

Author:
leo

Field Summary
 ArrayList<String> lines
           
 
Constructor Summary
InfoSilkGenerator()
           
 
Method Summary
 void addLine(String text)
           
 List<String> getLines()
           
 String getSilk()
           
 void visitBEDGene(BEDGene g)
           
 void visitGap(Gap g)
           
 void visitGraph(GraphData graph)
           
 void visitInterval(Interval interval)
           
 void visitRead(Read r)
           
 void visitReadCoverage(ReadCoverage readCoverage)
           
 void visitReadList(ReadList readList)
           
 void visitSAMRead(SAMRead r)
           
 void visitSAMReadLight(SAMReadLight r)
           
 void visitSAMReadPairFragment(SAMReadPairFragment fragment)
           
 void visitSequence(ReferenceSequence referenceSequence)
           
 
Methods inherited from class org.utgenome.gwt.utgb.client.bio.GenomeRangeVisitorBase
visitDefault, visitGene, visitSAMReadPair
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

lines

public ArrayList<String> lines
Constructor Detail

InfoSilkGenerator

public InfoSilkGenerator()
Method Detail

getSilk

public String getSilk()

getLines

public List<String> getLines()

addLine

public void addLine(String text)

visitBEDGene

public void visitBEDGene(BEDGene g)
Specified by:
visitBEDGene in interface GenomeRangeVisitor
Overrides:
visitBEDGene in class GenomeRangeVisitorBase

visitGap

public void visitGap(Gap g)
Specified by:
visitGap in interface GenomeRangeVisitor
Overrides:
visitGap in class GenomeRangeVisitorBase

visitInterval

public void visitInterval(Interval interval)
Specified by:
visitInterval in interface GenomeRangeVisitor
Overrides:
visitInterval in class GenomeRangeVisitorBase

visitRead

public void visitRead(Read r)
Specified by:
visitRead in interface GenomeRangeVisitor
Overrides:
visitRead in class GenomeRangeVisitorBase

visitSAMRead

public void visitSAMRead(SAMRead r)
Specified by:
visitSAMRead in interface GenomeRangeVisitor
Overrides:
visitSAMRead in class GenomeRangeVisitorBase

visitSAMReadLight

public void visitSAMReadLight(SAMReadLight r)
Specified by:
visitSAMReadLight in interface GenomeRangeVisitor
Overrides:
visitSAMReadLight in class GenomeRangeVisitorBase

visitSequence

public void visitSequence(ReferenceSequence referenceSequence)
Specified by:
visitSequence in interface GenomeRangeVisitor
Overrides:
visitSequence in class GenomeRangeVisitorBase

visitReadCoverage

public void visitReadCoverage(ReadCoverage readCoverage)
Specified by:
visitReadCoverage in interface GenomeRangeVisitor
Overrides:
visitReadCoverage in class GenomeRangeVisitorBase

visitSAMReadPairFragment

public void visitSAMReadPairFragment(SAMReadPairFragment fragment)
Specified by:
visitSAMReadPairFragment in interface GenomeRangeVisitor
Overrides:
visitSAMReadPairFragment in class GenomeRangeVisitorBase

visitGraph

public void visitGraph(GraphData graph)
Specified by:
visitGraph in interface GenomeRangeVisitor
Overrides:
visitGraph in class GenomeRangeVisitorBase

visitReadList

public void visitReadList(ReadList readList)
Specified by:
visitReadList in interface GenomeRangeVisitor
Overrides:
visitReadList in class GenomeRangeVisitorBase


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